Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins

We here report statistical analyses of 76 families of integral outer membrane pore-forming proteins (OMPPs) found in bacteria and eukaryotic organelles. 47 of these families fall into one superfamily (SFI) which segregate into fifteen phylogenetic clusters. Families with members of the same protein size, topology and substrate specificities often cluster together. Virtually all OMPP families include only proteins that form transmembrane pores. Nine such families, all of which cluster together in the SFI phylogenetic tree, contain both α- and β-structures, are multi domain, multi subunit systems, and transport macromolecules. Most other SFI OMPPs transport small molecules. SFII and SFV homologues derive from Actinobacteria while SFIII and SFIV proteins derive from chloroplasts. Three families of actinobacterial OMPPs and two families of eukaryotic OMPPs apparently consist primarily of α-helices (α-TMSs). Of the 71 families of (putative) β-barrel OMPPs, only twenty could not be assigned to a superfamily, and these derived primarily from Actinobacteria (1), chloroplasts (1), spirochaetes (8), and proteobacteria (10). Proteins were identified in which two or three full length OMPPs are fused together. Family characteristic are described and evidence agrees with a previous proposal suggesting that many arose by adjacent β-hairpin structural unit duplications.

本研究针对细菌及真核细胞器中发现的76个整合型外膜孔蛋白（integral outer membrane pore-forming proteins, OMPPs）家族开展统计分析。其中47个家族隶属于1个超家族（SFI），该超家族可进一步划分为15个系统发育簇。成员蛋白尺寸、拓扑结构及底物特异性一致的家族通常会聚集于同一簇中。几乎所有OMPPs家族仅包含形成跨膜孔的蛋白。有9个此类家族均聚集于SFI系统发育树中，它们同时包含α与β结构，属于多结构域、多亚基系统，且负责转运大分子物质。其余绝大多数SFI家族的OMPPs则负责转运小分子物质。SFII及SFV同源蛋白来源于放线菌门，而SFIII与SFIV家族蛋白则来源于叶绿体。3个放线菌门OMPPs家族及2个真核OMPPs家族主要由α螺旋（α-TMSs）构成。在71个（推定）β桶状OMPPs家族中，仅有20个无法被划归至任何超家族，这些家族主要来源于放线菌门（1个）、叶绿体（1个）、螺旋体门（8个）及变形菌门（10个）。本研究还鉴定出由2个或3个全长OMPPs融合形成的蛋白。本研究对各家族的特征进行了描述，相关证据支持此前一项假说，即多数OMPPs家族起源于相邻β发夹结构单元的重复复制事件。